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|
%global _empty_manifest_terminate_build 0
Name: python-cbgen
Version: 1.0.2
Release: 1
Summary: Python wrapper around a BGEN library
License: MIT
URL: https://github.com/limix/cbgen
Source0: https://mirrors.nju.edu.cn/pypi/web/packages/4b/ea/76eb6a4361bb5927ff29a96baf5668296905bdffe90cc31e692728fc3574/cbgen-1.0.2.tar.gz
BuildArch: noarch
Requires: python3-appdirs
Requires: python3-build
Requires: python3-cffi
Requires: python3-numpy
Requires: python3-pooch
Requires: python3-pytest
Requires: python3-toml
%description
# cbgen
Python wrapper around a BGEN library.
([cbgen documentation](https://cbgen.readthedocs.io)).
[BGEN](https://www.well.ox.ac.uk/~gav/bgen_format/) is a file format for
storing large genetic datasets. It supports both unphased genotypes and phased
haplotype data with variable ploidy and number of alleles. It was designed to
provide a compact data representation without sacrificing variant access
performance. This Python package is a wrapper around the [bgen
library](https://github.com/limix/bgen), a low-memory footprint reader that
efficiently reads bgen files. It fully supports the bgen format specifications:
1.2 and 1.3; as well as their optional compressed formats.
## Installation
```bash
pip install cbgen
```
## Usage example
```python
>>> import cbgen
>>>
>>> bgen = cbgen.bgen_file(cbgen.example.get("haplotypes.bgen"))
>>> bgen.create_metafile("haplotypes.bgen.metafile")
>>> mf = cbgen.bgen_metafile("haplotypes.bgen.metafile")
>>> print(mf.npartitions)
1
>>> print(mf.nvariants)
4
>>> print(mf.partition_size)
4
>>> part = mf.read_partition(0)
>>> gt = bgen.read_genotype(part.variants.offset[0])
>>> print(gt.probability)
[[1. 0. 1. 0.]
[0. 1. 1. 0.]
[1. 0. 0. 1.]
[0. 1. 0. 1.]]
>>> mf.close()
>>> bgen.close()
```
## Authors
* [Carl Kadie](https://github.com/CarlKCarlK)
* [Danilo Horta](https://github.com/horta)
## License
This project is licensed under the [MIT License](https://raw.githubusercontent.com/limix/cbgen/main/LICENSE).
%package -n python3-cbgen
Summary: Python wrapper around a BGEN library
Provides: python-cbgen
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-cbgen
# cbgen
Python wrapper around a BGEN library.
([cbgen documentation](https://cbgen.readthedocs.io)).
[BGEN](https://www.well.ox.ac.uk/~gav/bgen_format/) is a file format for
storing large genetic datasets. It supports both unphased genotypes and phased
haplotype data with variable ploidy and number of alleles. It was designed to
provide a compact data representation without sacrificing variant access
performance. This Python package is a wrapper around the [bgen
library](https://github.com/limix/bgen), a low-memory footprint reader that
efficiently reads bgen files. It fully supports the bgen format specifications:
1.2 and 1.3; as well as their optional compressed formats.
## Installation
```bash
pip install cbgen
```
## Usage example
```python
>>> import cbgen
>>>
>>> bgen = cbgen.bgen_file(cbgen.example.get("haplotypes.bgen"))
>>> bgen.create_metafile("haplotypes.bgen.metafile")
>>> mf = cbgen.bgen_metafile("haplotypes.bgen.metafile")
>>> print(mf.npartitions)
1
>>> print(mf.nvariants)
4
>>> print(mf.partition_size)
4
>>> part = mf.read_partition(0)
>>> gt = bgen.read_genotype(part.variants.offset[0])
>>> print(gt.probability)
[[1. 0. 1. 0.]
[0. 1. 1. 0.]
[1. 0. 0. 1.]
[0. 1. 0. 1.]]
>>> mf.close()
>>> bgen.close()
```
## Authors
* [Carl Kadie](https://github.com/CarlKCarlK)
* [Danilo Horta](https://github.com/horta)
## License
This project is licensed under the [MIT License](https://raw.githubusercontent.com/limix/cbgen/main/LICENSE).
%package help
Summary: Development documents and examples for cbgen
Provides: python3-cbgen-doc
%description help
# cbgen
Python wrapper around a BGEN library.
([cbgen documentation](https://cbgen.readthedocs.io)).
[BGEN](https://www.well.ox.ac.uk/~gav/bgen_format/) is a file format for
storing large genetic datasets. It supports both unphased genotypes and phased
haplotype data with variable ploidy and number of alleles. It was designed to
provide a compact data representation without sacrificing variant access
performance. This Python package is a wrapper around the [bgen
library](https://github.com/limix/bgen), a low-memory footprint reader that
efficiently reads bgen files. It fully supports the bgen format specifications:
1.2 and 1.3; as well as their optional compressed formats.
## Installation
```bash
pip install cbgen
```
## Usage example
```python
>>> import cbgen
>>>
>>> bgen = cbgen.bgen_file(cbgen.example.get("haplotypes.bgen"))
>>> bgen.create_metafile("haplotypes.bgen.metafile")
>>> mf = cbgen.bgen_metafile("haplotypes.bgen.metafile")
>>> print(mf.npartitions)
1
>>> print(mf.nvariants)
4
>>> print(mf.partition_size)
4
>>> part = mf.read_partition(0)
>>> gt = bgen.read_genotype(part.variants.offset[0])
>>> print(gt.probability)
[[1. 0. 1. 0.]
[0. 1. 1. 0.]
[1. 0. 0. 1.]
[0. 1. 0. 1.]]
>>> mf.close()
>>> bgen.close()
```
## Authors
* [Carl Kadie](https://github.com/CarlKCarlK)
* [Danilo Horta](https://github.com/horta)
## License
This project is licensed under the [MIT License](https://raw.githubusercontent.com/limix/cbgen/main/LICENSE).
%prep
%autosetup -n cbgen-1.0.2
%build
%py3_build
%install
%py3_install
install -d -m755 %{buildroot}/%{_pkgdocdir}
if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
pushd %{buildroot}
if [ -d usr/lib ]; then
find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/lib64 ]; then
find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/bin ]; then
find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/sbin ]; then
find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
fi
touch doclist.lst
if [ -d usr/share/man ]; then
find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
fi
popd
mv %{buildroot}/filelist.lst .
mv %{buildroot}/doclist.lst .
%files -n python3-cbgen -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Fri May 05 2023 Python_Bot <Python_Bot@openeuler.org> - 1.0.2-1
- Package Spec generated
|
